Contacts of the helix formed by residues 9 - 24 (chain B) in PDB entry 1XFB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 9 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B PRO* 6.0 0.4 - - - -
8B LEU* 1.3 76.9 - - - +
10B ALA* 1.3 64.5 + - - +
11B GLU* 3.3 14.4 + - - +
12B GLN* 2.6 41.9 + - - +
13B LYS* 3.0 23.6 + - - +
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Residues in contact with ALA 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B SER* 1.3 74.4 - - - +
11B GLU* 1.3 68.8 + - + +
13B LYS* 3.4 11.9 + - - +
14B LYS* 3.1 23.0 + - - +
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B SER* 3.6 13.7 - - - +
10B ALA* 1.3 79.8 - - + +
12B GLN* 1.3 64.8 + - + +
14B LYS* 3.1 10.0 - - - +
15B GLU* 3.0 21.9 + - - +
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Residues in contact with GLN 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ALA 4.2 2.1 + - - +
8B LEU* 3.3 26.8 - - + +
9B SER* 2.6 42.8 + - - +
11B GLU* 1.3 75.7 - - + +
13B LYS* 1.3 66.6 + - - +
15B GLU* 3.2 12.5 + - - +
16B LEU* 3.0 29.0 + - + +
179B GLN 5.4 1.5 + - - +
180B GLN* 4.8 11.5 + - - +
182B GLY* 6.0 2.2 - - - +
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Residues in contact with LYS 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.8 33.2 - - + +
9B SER 3.0 20.0 + - - +
10B ALA* 3.7 9.9 - - - +
12B GLN* 1.3 75.5 - - - +
14B LYS* 1.3 63.4 + - - +
16B LEU* 3.3 1.0 + - - +
17B SER* 2.9 21.8 + - - -
223B TYR* 3.3 53.2 - - + +
259C ARG* 4.3 17.9 - - - +
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Residues in contact with LYS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ALA 3.1 14.0 + - - +
11B GLU* 3.1 14.1 + - - +
13B LYS* 1.3 75.6 - - - +
15B GLU* 1.3 66.8 + - - +
17B SER* 3.0 13.6 + - - -
18B ASP* 2.8 55.0 + - - +
223B TYR* 5.2 0.6 + - - -
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLU 3.0 8.8 + - - +
12B GLN* 3.6 14.6 - - - +
14B LYS* 1.3 78.6 - - - +
16B LEU* 1.3 63.3 + - + +
18B ASP* 3.5 7.9 + - - +
19B ILE* 2.9 44.2 + - + +
139B LYS* 2.9 31.0 + - - -
182B GLY* 4.1 15.7 - - - +
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.5 33.2 - - + -
12B GLN* 3.0 16.8 + - + +
13B LYS 3.6 5.8 - - - +
15B GLU* 1.3 76.3 - - + +
17B SER* 1.3 63.8 + - - +
19B ILE* 3.2 3.2 + - + -
20B ALA* 2.9 20.8 + - - +
179B GLN* 3.8 28.7 - - + +
182B GLY* 3.7 11.7 - - - +
183B ILE 3.6 42.6 - - - +
184B VAL* 3.2 18.5 - - + +
223B TYR* 4.3 2.9 - - + -
226B GLY* 4.0 15.0 - - - +
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Residues in contact with SER 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LYS 2.9 17.4 + - - -
14B LYS* 3.5 12.7 + - - -
16B LEU* 1.3 77.2 - - - +
18B ASP* 1.3 65.6 + - - +
20B ALA* 3.2 2.6 + - - +
21B LEU* 3.0 40.4 + - - +
223B TYR* 4.2 10.3 - - - -
225B GLU* 3.5 27.3 + - - +
226B GLY* 4.3 0.2 - - - -
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Residues in contact with ASP 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LYS* 2.8 48.8 + - - +
15B GLU* 3.8 6.7 + - - +
17B SER* 1.3 76.9 + - - +
19B ILE* 1.3 66.1 + - + +
21B LEU* 2.9 13.8 + - - +
22B ARG* 2.9 32.1 + - + +
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Residues in contact with ILE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLU* 2.9 29.3 + - + +
16B LEU* 3.5 4.0 - - - +
18B ASP* 1.3 76.9 - - + +
20B ALA* 1.3 64.1 + - - +
22B ARG* 3.3 16.2 + - - +
23B ILE* 3.1 40.5 + - + +
104B VAL* 4.2 5.6 - - + -
139B LYS* 3.7 19.7 - - - +
144B ASP* 3.5 52.3 - - + +
182B GLY 4.1 3.8 - - - +
184B VAL* 3.6 9.9 - - + -
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU 2.9 13.8 + - - +
17B SER 3.4 8.5 - - - +
19B ILE* 1.3 77.1 - - - +
21B LEU* 1.3 62.1 + - - +
23B ILE* 3.2 17.5 + - - +
24B VAL* 3.2 18.4 + - - +
184B VAL* 4.2 21.1 - - + -
225B GLU 4.1 6.7 - - - +
226B GLY* 4.6 0.7 - - - -
227B THR 4.4 2.7 - - - +
228B LEU* 4.5 4.9 - - + +
266B PRO* 3.8 24.7 - - + -
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B SER* 3.0 33.6 + - - +
18B ASP* 2.9 10.8 + - - +
20B ALA* 1.3 73.8 - - - +
22B ARG* 1.3 66.1 + - - +
24B VAL* 3.6 7.0 - - + -
25B ALA* 2.9 25.6 + - - +
266B PRO* 3.8 26.7 - - + +
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Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ASP* 2.9 23.4 + - + +
19B ILE* 3.7 18.3 - - - +
21B LEU* 1.3 78.0 - - - +
23B ILE* 1.3 64.7 + - - +
25B ALA* 3.3 16.9 + - - +
28B LYS* 4.2 6.9 - - - +
75B GLY* 4.3 3.7 - - - +
102B GLY* 3.0 32.9 + - - -
103B ILE 4.6 2.0 + - - -
104B VAL* 3.8 28.6 - - + +
144B ASP* 5.2 5.9 + - - -
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Residues in contact with ILE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE* 3.1 24.5 - - + +
20B ALA* 3.2 7.6 + - - +
22B ARG* 1.3 79.5 - - - +
24B VAL* 1.3 59.7 + - + +
25B ALA 3.4 1.7 + - - -
28B LYS* 3.9 9.0 - - - +
29B GLY* 4.5 2.4 - - - +
30B ILE* 3.6 37.2 - - + +
75B GLY* 3.6 21.0 + - - +
76B GLY* 4.4 7.0 - - - +
104B VAL* 3.7 17.7 - - + -
145B PHE* 3.5 43.1 - - + -
184B VAL* 5.2 1.1 - - + -
228B LEU* 4.0 15.9 - - + -
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Residues in contact with VAL 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ALA 3.2 14.8 + - - +
21B LEU* 3.6 12.6 - - + +
23B ILE* 1.3 76.8 - - + +
25B ALA* 1.3 68.9 + - - +
26B PRO* 3.5 2.1 - - - +
28B LYS 4.5 5.8 - - - -
30B ILE* 6.0 0.4 - - + -
228B LEU* 3.7 26.0 - - + -
266B PRO* 4.2 17.3 - - + +
267B GLY* 4.2 6.5 - - - -
268B VAL 5.0 0.4 - - - +
269B THR* 3.8 22.4 - - + -
297B ALA* 3.7 31.5 - - + +
299B THR* 4.3 11.1 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il